


New Doubts

by Tdelicot



Category: X Files
Genre: F/M
Language: English
Status: In-Progress
Published: 2016-10-13
Updated: 2016-11-15
Packaged: 2018-08-22 02:52:19
Rating: Mature
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 9
Words: 5,373
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/8269901
Author URL: https://archiveofourown.org/users/Tdelicot/pseuds/Tdelicot
Summary: In the light of her brother's issues after finding out about the metal chip taken out of his neck. Dana Scully and others are having doubts.





	1. Chapter 1

In the light of her brother Bill and his recent troubles. For which he's still trying to understand the reasoning as to why. The Consortium would want to have him involved in their plans.

For years William Scully didn't care either way. As to what his sister would be doing working for the F.B.I. and the X Files department. And most of all "Spooky Mulder" his nick name from those working with him in the past years.

Even his own sister had doubts about working with Mulder in the very beginning. But now here it is some 25 years later. Back together in mind and body as partners and in marriage.

Along with the general facts fighting once more C.G. Spender and the new Consortium. In conjunction with the project having to start up with all new aliens involved.

There has been a number of times Dana Scully had inquired about her brother's activities with his job. Always being on the road for his company.

However recently having found out about her brother having been taken years ago. Only to be used as a "Sleeper" of sorts. In order to gain further access into the workings of the X Files department and any type of alien activities on their part.

It would be ironic on their part. Never knowing these facts until recently with the removal of the chip in the back of his neck. And without his general knowledge until the dreams started as with the images.

It had to be a true metaphor of things to come for Bill Scully and the members of the X - Files department. And Spender's appetite to destroy Fox Mulder in the process. His one and only revenge to get some what even with his meddling years ago with shutting down the project the first time.

And with trying to separate the difference with Bill Scully of what those images had meant in general. He needed with satisfaction once given the answers to what his true purpose would be with his life and those of the Consortium.

Even though. He wanted no part of it until recently to look for the reasons. To why he'd to be part of the plans against his better judgement. Until Fox Mulder's own son and his rebels finding out the truth about his true nature and involvement.

Leading to the abstract issues of ever doubting the man once again. And alleviate the troubles brewing from with-in the project and the new alien race. Wishing to destroy Earth and the surrounding planets in the solar system and beyond.

And now only to find out with recent etchings from a return Miles Davies. For where he was abducted with Fox Mulder many years ago. That a new alien race from outside our own galaxy and beyond. To be some how involved without even knowing these facts through either Davies and Bill Scully.

Neither understanding the true nature of the images and their meanings. Which will be disastrous for everyone involved.

However for now Bill Scully after finding the warehouse and speaking with Dr. Barrows. And his need to keep his secret from C.G.Spender and the members of the Consortium. Only to find that the gene sequence program to build further Super Humans is failing due to some type of antibody and toxic with-in the blood system of the donor sperms/eggs.

Though his plan coming from Bill Scully would be to seek out Spender and any of the new alien race involved. Seeking out. Otherwise he'd no idea what his remaining part of the plan would be like in the long run.

Thinking to himself heading back to his hotel room after speaking with Barrows and the evidence in general.

He needed to be sure. He was going to be protected from those over head in Earth's atmosphere. William, his rebels and his space craft supposed to be using their cloaking device to be hiding the vessel from Spender and the Bounty Hunter.

Hoping and praying for the best at this point in time. He would be able to come to terms with his plan in the long run. And show his sister and Fox Mulder. He would finally have the guts to finish this right to the very end. No matter what the out-come will be.


	2. Chapter 2

For Bill Scully currently inside of his motel room. After coming back from the warehouse and meeting up with Dr. Barrows.

For which he was taking a huge gambit at that particular time. Even though Bill Scully getting the information was needed for all involved.

There would be only a number of things going wrong for the project. When in fact finding the sperm/egg samples were tainted with some sort of an virus. In order to develop a new super human. Along with the total aspect of the project that certain gene cells used were not suitable for the scientists purposes.

However this in fact given to Fox Mulder and his sister of the X- Files department. They would tell him to leave it along for now. While he could be working on his own work for his company.

Currently he would be working with a new client. Involving a new-rust product for where the client paid the company a fortune to come up with something new and inventive for his customers.

Taking the proper time to discuss it over the phone. Before going to meet with the client tomorrow morning at his local office some ten miles from his motel room. Scully hopefully would be thinking about whether it was going to be really hot & humid once again for this time of the year.

Going over to turn up the air conditioning from inside of his motel room. He would be feeling some what warm for the most part. He was in need to call his sister Dana back in Washington, D.C. after flying back and receiving the information from Dr. Barrows.

But knowing the time difference at this point. He would call her sometime tomorrow after meeting up with his client.

Even though he knows. His own sister and Fox Mulder would be having those doubts still. On whether or not he could be trusted after what had happened to him. With finding the metal chip from behind his neck by Allysa on board William's rebel space craft.

********************************************************

The next morning after having a quiet evening for the most part. After waking some what refreshed with his sleep. Along with taking a hot shower to loosen up his muscles. Though years ago it would be much easier to get up and just go quickly.

He gets ready to leave to meet up with the client. Making sure all was in order with his brief case and other essentials needed. Mostly his lap top for which the designs are enclosed with the software used.

The best available on the market for when it comes to Microsoft products and virus protection.

Once this was done. He felt satisfied all was in order for his meeting. Before heading out into the heat of the dessert.


	3. Chapter 3

Thank god for the air conditioning. He was hot and humid outside. Usually it would be a dry sort of heat. But today it was different. At least he's going to be inside of the office building to meet with his client.

However this time. His mind would be wondering a bit. Needing to watch his step with driving his vehicle. He doesn't need to get himself into an accident at this point.

Moving to the side of the road for a moment to gather up his thoughts. After checking for any traffic behind him. He would be able to push forward to head out for his destination.

And when he did with taking his time. His mind would be going the details of his plan and what he's going to say to prove his point of the ad. It's why he's been with the position for so long.

After a while. Its almost like being a part of the woodwork for when it comes to doing the job.

Just like with his sister Dana and Fox Mulder for when it comes to the X Files department. You can only do so much before the job becomes some what boring. Its never been the case with him over the years.

Always trying to come up with new ways and very invented coming from his brain and of his associates. Maybe its why he never married. Always having to be on the road and working constantly to prove himself on every level.

However. What does he has to show for it at this time of his life? Besides having a mother that is dead. And his sister Dana always proving to be the best available in the field of medicine and of the X files section for the F.B.I.

At least he's alive right now. For how long. He won't know the answer. Unless C.G. Spender and the bounty hunter gets a hold of him later on down the line.

Checking the GPS for the last time. He will be arriving some time with-in the next few moments. Taking in a deep sigh to relax.

He was able to see the office building for where his client stayed for this trip to work on the final stage.

Looking both sides of the road in order to drive across into the parking section of the building. There wasn't many cars at this time of the day. To be some what usual. Slowly moving in with the vehicle. He needed to be close to the entrance without having to walk all that far.

Checking for his brief case and other essentials. He turns off everything inside of the rented vehicle. Before he's able to move on outside and taking the elevator to the fourth floor.

It was very cool inside. With the air conditioning working hard to cool off everyone in the building.

Once stepping out of the elevator. He's able to stop off at the main desk. Letting know the secretary that Bill Scully is here to see his client. He gives the name of the client and his I.D. with the company he works for.

It was at this moment. When the secretary tells him. He can go right into his office. As everyone was waiting for him with his ideas on the new product.

Checking himself for the last time. He takes a deep breath before slowly moving over to the door and knocking. He is told by some one on the other side of the door to come on in and be seated.


	4. Chapter 4

Walking into the office to meet with the client. Grayson in his early fifties was mostly pleased to see Bill Scully. Placing all of his faith into the man to come up with something new and inventive for his company.

He was removing the graphic designs of the ads that will be used was very interesting never the less. When he took them out to show Grayson and placing the designs onto the gray coffee table in front of the desk.

Grayson was impressed with Scully and of his designs. While he was looking over at his two associates in the far corner. Nodding his head with the approval.

While giving Bill Scully the time to discuss the ads further in general detail on all levels. It was a few minutes later Grayson takes the water pitcher on the desk to pour the glass. Asking on whether Scully was interested in a glass as well.

He agreed to the request having to be really dry with his throat. After a few moments with drinking the cold liquid to feeling better in general.

But was he really! 

All of a sudden. His mind started to drift as if he was in another reality of sorts. Hearing the voices in an around him. He was trying to focus on the one single voice. It sounded like Grayson calling out to him.

When he did open his eyes. He wasn't in the office with his client. But rather on some alien space craft laying on the slab table once again.

How could this be once again. Unless he was having some sort of an relapse or again having one of those dream images. He didn't know either way.

Taking the time to gather up his thoughts for the moment. He waited until the dizziness had gone away for the most part.

He couldn't believed it. He was back on the vessel once more on some sort of a slab table.

When he saw that it was inside the ship. He saw Grayson coming around to face him after speaking with the others from behind.

"Welcome back Mr. Scully. You finally made it back after some time away from us." He says to Bill Scully before changing into the bounty hunter.

It was at this time. When he saw that the probe coming towards him. Scully was trying to break away from his binds. Only to cause his wrists to start to bleed. Seeing it coming closer and closer to him. He started to scream out on the table. While the bounty hunter told the others in the back of him. "Just be sure to speed up the process. I need to know for sure just where are Fox Mulder and Dana Scully and his son's vessel."

As the one single probe continued to come closer and closer to him. While Bill Scully kept on screaming out before finally passing out.

Moments later.............

Bill Scully was finding himself back again. In the office with his client. And hearing of the words. Exhaustion. It was a whopper of an nightmare. After feeling the weakness over take him.

While Grayson telling him relax for a few moments before getting up from the couch. And wishing to know just what exactly happened. In order for him to pass out like that.

It was Grayson had asked him on just was the last thing he'd remembered.

"I was feeling some what dizzy and feeling like I was elsewhere for those few seconds. It was so real for what my brain was telling me." He said disoriented some what.

"You seem to be fine now. I suggest Mr. Scully. You take it easy. Other wise you sold me and my associates on the new ads for the new rust product. I will certainly call my boss and tell him the good news. No doubt he will probably be calling you soon to congratulate you for a job well done on selling the product."

"Hopefully Mr. Grayson. Your customers will be happy as well with wanting to purchase the products at a reasonable price." Taking in a deep breath before moving off his couch without having to be dizzy once again.

However this time he was feeling better, and without an issue of weakness. 

"Lets hope so. I would of hated to waste your time and our efforts in coming here in the first place. Along with the company spending a enormous amount of monies for when it comes to the ads."

"No doubt. Any rate I will leave to your other business Mr. Grayson. Thanks." He moves over to him to shake his hand as well with the two other gentlemen standing in the corner. "Take care." He says before opening the door and leaving.

It was at this time when Grayson turning into the bounty hunter. He would asked on whether they were able to retrieve the information from his brain.

The first gentleman said the following. "I am afraid now. It would seem to be he was some how blocking that part of his memories."

"How is this possible?" He asked while sneering at the two.

"It would seem someone or something from another source has this ability to block out any intrusion."

"I need to know the answer. And quite soon before the next wave of our ships start to come through the worm hole to begin the attack." While the bounty hunter said to the two before packing up his things and transporting back up to there cloaked space craft.

"Yes sir. right away."


	5. Chapter 5

As soon as Bill Scully arrived back at his motel room. Taking out his cell phone. Even though he didn't know on the transceiver inside of his contacts were still working. Sending signals back to the Lone Gunmen's hide out.

Using the phone was better. Since he's not able to trust anyone or anything for the moment. After what had happened earlier. Finding himself back on board the space craft as a pawn. Just like in a chess match.

He was able to call Fox Mulder. Using a special coded text devised by the Gunmen. He was able to tell them. He'd made some type of contact by the bounty hunter. In disguise as Mr. Grayson for the company he was able to come up with the ads.

For now. He will mostly keep it low-key. In order to protect himself and those involved with the plan. Whether or not it works. It will certainly all depends on time and or on whether just where the bounty hunter's space craft would be located.

In order to give time for the rebels to arrive back into Earth's orbit and prepared themselves.

***************************************************************

As soon as the Lone Gunmen received the text message. While placing in the proper coding.

They were able to connect into the transceiver and see what exactly Bill Scully was seeing at the time of his black out.

Since now all three of the Lone Gunmen were watching the view screen to see the images to come up. Along with shaking their heads.

Bill Scully in fact was actually abroad the space craft having to be probed for information. And the one key figure with-in the Consortium would be the Bounty Hunter.

They were able to hear of the following. " I need to know the location of Fox Mulder and Dana Scully." There be three different facial expression from the gunmen inside of their hideout for now.

In order to truly understand. Just what exactly was happening from the images.

Barrows would asked on how this was possible. When the Bounty Hunter knows where they are in the first place.

The third new member Baxter asked on whether it might be some sort of a deception on their part.

Answering back taking the very moment to think of an reply. "Unless they are looking for someone else entirely." She says to have them think further in regard to the total scenario.

"I would think so. But it just doesn't follow right now." Barrows interjected with her response from the printer. And besides. Bill Scully was in their hands. But yet they let him go for the most part. Only to once again to take him abroad. Just maybe they are trying to test his abilities and or he's loyal to his sister Dana Scully.

"This I don't know everyone. But for now. We need to be very careful." Baxter said to his associates.

**************************************************

For Fox Mulder. He was being distracted by his own wife for the moment. Getting his mind off everything. He needs to at this point. However. He was trying to understand why she wasn't all too worried about her brother.

There was a possible chance he just might betray her in every way. But then again. They knew with going into this plan of her brothers. Just might actually back fire on them.

Hopefully very soon. William and his rebels will be arriving soon. After chasing some unknown space craft going into the worm hole. They had decided not to further pursue the craft. In order to head back to Earth and help his father and mother out once again with the new Consortium.

Laying together in bed. After going though the motions of having sex. Otherwise his mind. As it were for the moment. He just hasn't been able to emphasized just how important of finding out the total and complete truth.

Scully was trying to tell him to just relax afterwards. Even though she made the suggestion of taking a hot shower together. Just might do the trick.

"So. what will it be Mulder?" She asked tenderly touching his face and the stubble growing on his face. She would call it his "Midnight Shadow" instead of the usual saying.

He laughed finally. Along with saying. "I will join you in the shower." Before getting up from the bed. He's able to give his wife an arousing hard kiss to at least help make her feel some what better.

And it did. Almost to the point of being some what of an attack on his senses, mind and mostly his body.

Her appetite this evening would be unnerving for his normal taste from over the years. And this includes their very first time together so many years ago.

***************************************************

Sometime later

Laying in bed together. After the shower to relieve the tension of their bodies. Fox Mulder started to think otherwise further on the issue of hand. Involving his wife's brother and his behavior lately. Having conflicting interests to mostly unnerve anyone for when it comes to the Consortium and the project.

It did with him many years ago. For when it came to his sister Samantha and his quest to look for her. Until he found her years later with-in the twilight.

It'd made him think with a comment that was made recently. In order to understand the nature of Spender's quest. Just maybe the bounty hunter is not looking for him and Scully. But rather his sister Samantha. This fact doesn't make any sense. Since she is dead by the hands of Spender and the organization.

He'd to stop this way of thinking. It was mostly giving him some what of a headache. Looking over at his wife asleep on her side of the bed. He wanted to at least try to fall asleep. And if it doesn't work. There would be other options that just might help him in the short run.


	6. Chapter 6

Having fallen asleep. Even though Fox Mulder started to dream right away. Finding himself caught once again on the alien's slab table being probed once more for information.

He didn't know. In general what to say. Since his fear had taken over him for the moment. He needed to restrain himself in needing ventilation to breath.

He'd kept on hearing the same voice. Even though it wasn't Spender. Unless it was the bounty hunter. Mulder wasn't able to see them through the bright light in front of him.

He'd gone through all this years ago being inexplicably embarrassed with being tortured. What ever these aliens were doing to him. Was incredibly painful. He would scream out. With every nerve of his body burning. Including his penis. 

He cried out. As the probe moved in closer to his chest and stomach area to cut into deep opening his insides. He screamed further before passing out completely.

It was at this point of his dream. Fox Mulder woke. Screaming out from the so real images of the nightmare. Since it was only just that a nightmare.

He was still very much alive and in his own bed. Otherwise having to woken his wife Dana Scully from a sound sleep. It was basically obviously. He was in great distress from what ever type of nightmare he'd.

"Jeez. Mulder what the hell happened to you?" She asked etch in irritation. She could see. He was having issues again with the nightmare for the moment.

She would have to wait. In order for him to gain his bearings. Taking hold of his hand to feel it some what shaky and extremely cold.

"Nightmare Dana. It seem so real for when I was actually on board the alien vessel years ago." He says rather coldly.

"Well your not Fox. She takes his body into her arms to comfort him from the stress or rather his dilemma of being caught up once again with the Consortium. "Were you able to figure out what they were looking for with-in your nightmare?" She asked. As her adrenaline would be spiking to the highest level. And she needed to calm herself down. Before having further issues with her pregnancy.

"Information from what I gathered. However I'm wonderfully on whether this had to do with your brother Bill and his crazy scheme of his?" He advised her of his theory at this particular time.

"Interesting concept Mulder. Otherwise it's been some time. Since we'd heard from him or the Lone Gunmen. Maybe we will need to at least confirm with them. In regard to whether the tracking device with-in his contacts are working."

"I need to take a quick shower for now. Afterwards I will call them to find out just what the hell is actually going on with them and your brother."

Gently getting into the hot water cascading over his head and the rest of his tense body. Fox Mulder was able to relieve of of the stress from the flow of the hot water. Taking his time to wash down his entire body with the soap from the soap dish.

From over the years. He has the tendency to stare at his stomach and chest. For when he was first taken by the aliens. In order to probe, cut and torture him to no end during the time he'd gone missing. And leaving Dana Scully alone to search for him. With her help from A.D. Scanner, Doggett and several others from the F.B.I. Even though truly not believing the entire story in the first place. On just what exactly had happened to him.

Continuing to search at the scar marks for when he was cut open from top to bottom. It was truly amazing. On how he was able to survive in the first place after all of these years.


	7. Chapter 7

Mulder needed to get past all that. In order to stay with-in the normal realm of things. Since when his life has ever been normal? He could never ever remember. If there ever was a life past Samantha. Accept for when he joined the F.B.I. to meet up with Dana Scully and the X-Files department.

There has been just too many mysteries that needed to be solved from over the years. And with a number of them solved.

Any rate for now. Mulder needed to finish up with his shower. In order to try to call the Lone Gunmen. Along with his questions having to be on his mind for the moment.

Using the blue towel to dry off his head and body. He didn't need to be catching a cold from the draft inside. One thing for sure. He didn't need a lecture from any one. Including from his own wife/partner.

After stepping out of the bathroom to change into more comfortable. He needed to set his mind. In regard to what he's going to be asking the Lone Gunmen. Needing the questions that needed to be asked.

Moving into further of their bedroom. He takes out his cell phone to bring up the number for his friends.He would take a single quick breath. Before pressing the send button. In order to make the proper connection with them. And no doubt the call is going to be monitor by them. In order to protect themselves from any type of intruders.

It's what they do best. Security measures to the extreme. Especially if it does involved any government cover-ups. And its what got the first Lone Gunmen group killed in the first place. Getting so deeply involved with C.G. Spender, the aliens. And most of all the Bounty Hunter and his super soldiers.

**Notes for the Chapter:**

> This series will be ending with Chapter Nine. And will be posted on Fanfiction.net with a series called "In The Thrones Of Despair" with-in the next two weeks.


	8. Chapter 8

However for Bill Scully. He wasn't able to do much more. Other than to wait for further instructions for when it comes to his job in general.

Otherwise. For when it comes to C.G. Spender. It was obvious. Something was differently up with them. And no doubt he will be finding out soon. In regard to his fate none the less.

And after speaking with Dr. Barrows. He'd mention something about one of their projects. Was going to be moving to another location.

If this is the case. The only ones that will be able to do anything about it. Would have to be agent Fox Mulder, his sister Dana, The Lone Gunmen and his sister's boss Walter Skinner.

His plan. In order to search for the truth of the conspiracy. Even though they'd been using him mostly as a pawn. He even suggested at one time. To have himself quarantine. However that idea was shot down by his own sister. In order to protect him. And compensate in other areas of his life.

Like with his work in general. And having to always be traveling on the road. In order to survive financially. Not to the fact he's not starving. He has put away a generous amount of funds away in the bank, CD'S and stocks for the most part. He wasn't obsessed for when it came to money. Unlike Fox Mulder for when it comes to his obsession and the X-Files.

All this thinking from inside of his motel room. After getting back from his meeting with his client for the new rust product. Even though having to be a total ruse on the part of the Consortium and Spender. In order to gain further information from him in general.


	9. Chapter 9

There wasn't much more to do. Accept continue on with his life in general. Including the facts. He was able to do his work with the new ad campaign. Even though having to be some what of a ruse.

And advising his sister and Fox Mulder. With what exactly had gone down with him with the client. 

While taking everything into stride for the moment. In order to take it easy mostly now. Heading back outside and into his vehicle at the height of the heat from the desert sun. He was able to head back to his motel room. Getting back into his vehicle. Taking a deep breath just prior to turning on the air conditioning inside.

Afterwards just before moving out onto the highway. Bill Scully decided to check his phone messages and texts. There would be two coming from his sister and one from the Lone Gunmen.

Telling him to be extremely careful with his movements. Some time during the next few weeks. In regard to his work situation and who he will come in contact with any new clients.

He was the very key to the Consortium. But for now. Bill Scully had to figure out his next move. Just like a piece on the chess board.

Even his own sister had advised him of this particular aspect. Just like it was for her and Fox Mulder right from the very beginning. It would be a true metaphor on his account. And hopefully it won't get any worst in the long run. Like with the end of the world.

And what has happened inside the office. He'd to remember it wasn't really real for the most part. Unfortunately for him. It'd seem so real to him. Showing up again on the damn space vessel in ordered to be probed for valuable information.

For the like of him not really knowing anything else. As previous stated with his sister and Mulder. Or whether his plan was some what successful or what 's to come for when it comes to the alien invasion.

He just hopes to god that Mulder's son and his rebels will be able to fight them off to a certain extent. Until his remaining Alliance members will be arriving in time. In order to stop them further and from destroying every single living thing.

And with his analysis. There was nothing more to be done. Accept wait. Its exactly what he plans to do for now.

He starts to head out now for his hotel room.......

**Notes for the Chapter:**

> Final Chapter. This series of stories will be continued with IN THE THRONES OF DESPAIR and will be posted on Fanfiction.net.


End file.
